Designing and delivering bioinformatics project-based learning in East Africa

Background The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its goals and how experiential learning through mini projects enhances the acquisition of skills and collaboration. We continued to learn and grow through honest feedback and evaluation of the program, trainers, and modules, enabling us to provide robust training even during the Coronavirus disease 2019 (COVID-19) pandemic, when we had to redesign the program due to restricted travel and in person group meetings. Results In response to the pandemic, we developed a program to maintain “residential” training experiences and benefits remotely. We had to answer the following questions: What must change to still achieve the RT goals? What optimal platforms should be used? How would we manage connectivity and data challenges? How could we avoid online fatigue? Going virtual presented an opportunity to reflect on the essence and uniqueness of the program and its ability to meet the objective of strengthening bioinformatics skills among the cohorts of students using different delivery approaches. It allowed an increase in the number of participants. Evaluating each program component is critical for improvement, primarily when feedback feeds into the program's continuous amendment. Initially, the participants noted that there were too many modules, insufficient time, and a lack of hands-on training as a result of too much focus on theory. In the subsequent iterations, we reduced the number of modules from 27 to five, created a harmonized repository for the materials on GitHub, and introduced project-based learning through the mini projects. Conclusion We demonstrate that implementing a program design through detailed monitoring and evaluation leads to success, especially when participants who are the best fit for the program are selected on an appropriate level of skills, motivation, and commitment. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-024-05680-2.


Video Conferencing
Zoom Meetings was the agreed platform to conduct live classes, pieces of training and seminars.The pro package, which starts from USD 15 per month per host, will be used.EANBiT has access to a pro account, which will be used for the training.
Reasons for Choosing Zoom Meetings 1. Ease of use: Once installed by the user, the process of creating meetings, joining meetings, and participating in meetings is straightforward.The users do not require high technical skills to use Zoom effectively.Also, its popularity has made it a common choice for many meetings meaning that more people are familiar with it.

Great design and development:
Zoom meetings is a well designed and developed platform with useful features depending on the package of choice.It is also mature for use across different platforms, i.e.Windows OS, Linux OS, Mac OS, Android and iOS.This makes Zoom work well across all these platforms without any functional differences, which is ideal for end-users.

Great Access Control:
Order is a prerequisite to a productive meeting.With a wellimplemented access control feature, Zoom Meetings allow for a defined group of users to control the meeting right from its creation through the meeting to the end.Features like waiting rooms improve security by allowing only known attendees to join the meeting, screen sharing restrictions, and muting and unmuting participants by the host.These features, among others, ensure a smooth meeting or training.

Additional File 1
Useful Features

Meeting Scheduling
Hosts can schedule meetings and send calendar updates and/or emails to the concerned participants.This feature will allow the calendar and meeting rooms for the different modules to be set in advance and the calendar shared in advance with the trainers and participants.The host also has excellent control of the meeting while creating it; like enforcing a waiting room for all participants, enforcing a password requirement for a meeting, muting participants on entry, enforcing no join before host, etc.Such features allow for better control of the meeting by the host.

I. File Transfer
Zoom allows for in-meeting file transfers with a limit file size of 512MB, allowing the instructor and the students to share materials during the live training.To make use of this feature, click on 'chat' and then 'file' to select a file to share from your computer.

II. Screen Sharing
Zoom allows participants to share their screens, making it easier for participants to participate in demos and presentations from their machines.Select the green Share Screen button then you can choose on the screen to share: a presentation, browser, or whiteboard (see below).

III. White Board
To create a classroom experience, allow for note-taking and scribbling, Zoom provides access to the whiteboard from the Share screen options.The whiteboard can be saved as png.For the best experience, you can use a stylus or a touch screen.Zoom also allows you to annotate over your slides.

IV. Chats
Participants can chat with one another during the training.This feature can be useful if participants want some help or clarification on some point, which they can get without necessarily disrupting the meeting or leaving the platform. V.

Meeting Recordings
Zoom allows the host to record the meeting for future reference if needed.The process is simple and only requires the host to click the record button, then zoom will take care of the rest.At the end of the meeting, Zoom saves meeting recordings in different formats; audio files (mp3, m4a, m3u) and video files (mp4).

VI. Breakout rooms
Zoom allows meeting organizers to create independent rooms.These can be used for group discussions or by teaching assistants to support smaller demos.

Contact Groups
Zoom allows one to create contacts and create a user group depending on the goals of the group.As such, group management is left to the Admin/ host, and zoom offers helpful features to support the admin.This feature is great for a classroom setup where students can be placed in contact groups for independent discussions.Contact groups can be added to a channel, which allows for quick meeting invites and chats that last beyond the meeting.

Communication, Discussions, and Collaboration
Slack was the agreed platform for student-teacher, student-student, and group collaboration.

Reasons for Choosing Slack
1. Ease of use: Slack uses the idea of a workspace to allow for collaborations.A workspace is created, and users are invited via email or link.Once onboard, they can decide what channels to join depending on their need.While on a channel, they can communicate with other users, and their chats will persist even after log-out.

Training Design:
The content of residential training informed our choice of Slack for collaboration.Students will spend a considerable amount of time doing a mini-project and also have other technical modules to tackle during the period of the training.Slack provides one of the best platforms for diverse collaborations, mainly by development teams for resolving technical issues.

Channels
This feature allows the workspace owner to create a separate place where a team can share messages, tools, and files.Channels can also be used for broadcasting information e.g.An announcement channel whereby only designated people can post but messages are received by all other people in the workspace.Special channels can be created to allow certain users to interact with one another in the form of a group set-up.

Direct Messages
This feature is perfect for conversations that don't require an entire channel to weigh in.Peerto-peer communications can be done through direct messages.

Mentions
For quicker responses from team members, one can mention a specific member starting with the @ symbol.A mention ensures the particular mentioned member is immediately notified.

Note Taking
Slack has a built-in note-taking option called posts.Posts enable team members to share and work together on items too big for messages.This is like a text document that team members can pass back and forth, like a simplified Google Documents.

Audio and video calls
Slack supports audio and video calls with up to 15 people.This feature is useful for afterclass follow-ups among students or students and trainers.

Content Management and Collaboration
GitHub was the agreed platform for sharing course material and content.Assignments, especially coding assignments and group projects, will be done from this platform.

Reasons for choosing GitHub
1. Content Management: GitHub provides a well-documented and straightforward way of managing content.Repositories are used for managing content, and this allows for changes to be made transparently.Also, the visibility of the repositories holding the content can be restricted to particular users.

Training Design:
The residential training has a mini-project and other technical modules.Most technical work and coding is best managed by git, a version control system.

Collaboration
Team members can easily collaborate on a coding project.Features offered by GitHub allows for seamless code reviews by team members making working on a single project by multiple users easier.Some of these features are;

I.
Reviewers: A student can request for peers to review a section of code or a push request.

II.
Customised comment: Reviewers can comment on a specific line in a specific file which makes the comment to have a better context thus well understood.

III.
Work branching: To ensure work is not derailed or new features are implemented simultaneously, branches are provided for this purpose.So students can be working on the same project but each handling a specific feature in their branch.This can also make teachers work easier where they can assess students depending on the work they are doing on their branches.

Cost Implications I. Using Zoom for Video Conferencing
Bandwidth requirements: Zoom recommends 1.2Mbps for upload and download of HD videos.Most ISPs provide on average speeds of between 9Mbps, download speed to 14Mbps for upload speed within Nairobi city.These speeds will differ from location to location, but on average, users of most telcos will get good speeds across the country with the best connectivity from Safaricom Ltd, Faiba, Airtel, and Telcom.If one is unsure of their These prices are not fixed and will vary depending on the package selected.

II. Using Slack and Git
These platforms do not consume as much data.Slack will mostly be used for collaboration using text as the main mode of communication.Text is usually the simplest data format to exchange and does not require high bandwidth or consume lots of data.Only files may consume more data depending on the type, content and size.
Git, on the other hand, consumes as much data as the content being shared.Our primary use for GitHub is content management especially Project collaborations, there are a few things that could be done to keep projects as small as possible.
1.Only track changes to your project and avoid, by all means, coupling the project and its environment together.Environments are usually very big yet are not special to a program, they can be recreated by other parties when guided how to do so.
2. Untrack files that are IDE specific.Some IDEs will create .ideafiles which details some specifics of the project while using that IDE.These are not necessary since different people might have different preferences on the IDE of choice.
connectivity, they can use these tools to check if they will have any issues participating in meetings; a. Speed Test Tools -Customised for Zoom meetings.b.Zoom Test Meeting -Good for testing how your internet would perform in case of a real meeting.It also gives you a chance to interact with the Zoom platform if you need to familiarize yourself with the available tools and features Zoom offers in isolation i.e. not in a real meeting environment.Zoom group meetings consume data as shown below.By default, Zoom uses the minimum available bandwidth.Also, HD video streaming is not enabled; most video calls will be between High Quality -720p.Thus, the average data usage per hour would range between 810MB -1.35GB.The usage may increase or decrease depending on how one uses the platform.Data usage may increase if one records a session with an additional 50MB per hour for voice recording and more for video recording.NB: Data usage may increase with the number of participants in the meeting, mostly because you might need to download more data compared to a smaller group.Here are some great tips to reduce data usage.
NB: Faiba may have a limitation i.e.A few phones can support it.Read more here.